DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Eocene-Oligocene diatoms in the western Indian Ocean

The occurrence of diatom species in the Eocene-Oligocene sections of Ocean Drilling Program (ODP) Leg 115 sites and Deep Sea Drilling Project (DSDP) Sites 219 and 236 in the low-latitude Indian Ocean are investigated. Diatoms are generally rare and poorly preserved in the Paleogene sequences we studied. The best-preserved assemblages are found close to ash layers in early Oligocene sediments. The low-latitude diatom zonation established for the Atlantic region by Fenner in 1984 is fully applicable to the Paleogene sequences of the western Indian Ocean. Correlation of the diatom zones to the calcareous nannofossil stratigraphy of the sites places the Coscinodiscus excavatus Zone of Fenner within calcareous nannofossil Subzone CP16b. For the Mascarene Plateau and the Chagos Ridge, the times when the sites studied, together with the areas upslope from them, subsided to below the euphotic zone are deduced from changes in the relative abundance between the group of benthic, shallow-water species and Grammatophora spp. vs. the group of fully planktonic diatom species. The Eocene section of Site 707, on the Mascarene Plateau, is characterized by the occurrence of benthic diatoms (approximately 10% of the diatom assemblage). These allochthonous diatoms must have originated from shallow-water environments around volcanic islands that existed upslope from ODP Site 707 in Eocene times. In Oligocene and younger sediments of Sites 707 and 706, occurrences of benthic diatoms are rare and sporadic and interpreted as reworked from older sediments. This indicates that the area upslope from these two Mascarene Plateau sites had subsided below the euphotic zone by the early Oligocene. Only Grammatophora spp., for which a neritic but not benthic habitat is assumed, continues to be abundant throughout the Oligocene sequences. The area of the Madingley Rise sites (Sites 709-710) and nearby shallower areas subsided below the euphotic zone already in middle Eocene times, as benthic diatoms are almost absent from these Eocene sections. Only sites located on abyssal plains, and which intermittently received turbidite sediments (e.g., Sites 708 and 711), contain occasionally single, benthic diatoms of Oligocene age. The occurrence of the freshwater diatom Aulacosira granulata in a few samples of late early Oligocene and late Oligocene age at Sites 707, 709, and 714 is interpreted as windblown. Their presence indicates at least seasonally arid conditions for these periods in the source areas of eastern Africa and India. Three new species and two new combinations are defined: Chaetoceros asymmetricus Fenner sp. nov.; Hemiaulus gracilis Fenner, sp. nov.; Kozloviella meniscosa Fenner, sp. nov.; Cestodiscus demergitus (Fenner) Fenner comb, nov.; and Rocella princeps (Jouse) Fenner comb. nov.

Calcareous nannofossil stratigraphy, mass accumulation rates and bulk density of sediments from ODP Leg 173 sites

Drilling on the Iberia Abyssal Plain during Ocean Drilling Program Leg 173 allowed us to recover Upper Cretaceous through Paleocene sediments at Sites 1068 and 1069 and only upper Paleocene sediments at Site 1067, which expands considerably the Upper Cretaceous to Paleocene record for this region. Of these three sites, Site 1068 recovered uppermost Cretaceous sediments as well as the most complete Paleocene record, whereas Site 1067 yielded only uppermost Paleocene sediments (Zone CP8). Site 1069 provided a rather complete upper Campanian through Maastrichtian section but a discontinuous Paleocene record. After a detailed calcareous nannofossil biostratigraphy was documented in distribution charts, we calculated mass accumulation rates for Holes 1068A and 1069A. Sediments in Hole 1068A apparently record the final stages of burial of a high basement block by turbidity flows. Accumulation rates through the Upper Cretaceous indicate relatively high rates, 0.95 g/cm**2/k.y., but may be unreliable because of the lack of datum points and/or possible hiatuses. Accumulation rates in the Paleocene section of Hole 1068A fluctuated every few million years from lower (~0.35 g/cm**2/k.y.) to higher rates (~0.85 g/cm**2/k.y.) until the latest Paleocene, when rates increased to an average of ~2.0 g/cm**2/k.y. Mass accumulation rates for the Upper Cretaceous in Hole 1069A indicate a steady rate of ~0.60 g/cm**2/k.y. from 75 to 72 Ma. There may have been one or more hiatuses between 72 and 68 Ma (combined Zone CC24 through Subzone CC25b), as indicated by the very low accumulation rate of 0.15 g/cm**2/k.y. The Paleocene section of Hole 1069A does not show the same continuous record, which may result from fluctuations in the carbonate compensation depth and poor recovery (average = 40%). Zones CP4 and CP5 are missing within a barren interval; this and numerous other barren intervals affect the precision of the nannofossil zonation and calculation of mass accumulation rates. However, in spite of these missing zones, mass accumulation rates do not seem to indicate the presence of hiatuses as the rates for this barren interval average ~1.0 g/cm**2/k.y. This study set out to test the hypothesis that a reliable biostratigraphic record could be constructed from sediments derived from turbidity flows deposited below the carbonate compensation depth. As illustrated here, not only could a reliable biostratigraphic record be determined from these sediments, but sedimentation and mass accumulation rates could also be determined, allowing inferences to be drawn concerning the sedimentary history of this passive margin. The reliability of this record is confirmed by independent verification by the establishment of a magnetostratigraphy for the same cores.

Diatom abundance in sediments from ODP Leg 167 sites

The Pliocene and Pleistocene periods are known for the onset and consequent amplification of glacial-interglacial cycles. The California margin, situated in the mid-latitudes of the northern Pacific Ocean, is expected to be one of the most interesting regions for Pliocene to Pleistocene paleoceanography because this area occupies a unique position in the ocean-atmosphere system over the region. In this study, we investigated paleoceanographic history, using fossil diatoms, since the Brunhes/Matuyama (B/M) paleomagnetic boundary in which glacial and interglacial periods began to alternate in 100-yr cycles. In Hole 1018A, to a depth corresponding to the beginning of Northern Hemisphere glaciation (late Pliocene), we investigated the responses of the ocean-atmosphere system to stepwise cooling in the California margin. Although the work is still continuing, this data report shows that fossil diatoms of Pliocene and Pleistocene sediments significantly changed both in quality and quantity and implies a possible relationship to global climatic changes.

Diatom biostratigraphy of the Kerguelen Plateau and Prydz Bay, Southern Ocean

Samples were examined for diatoms from 22 holes at 11 sites cored by ODP Leg 119 on the Kerguelen Plateau and in Prydz Bay, East Antarctica. Diatoms were observed in Oligocene through Holocene sediments recovered from the Kerguelen Plateau. The diatom flora from the Kerguelen Plateau is characterized by species such as Azpeitia oligocenica, Rocella gelida, Rocella vigilans, and Synedra jouseana in the Oligocene and Crucidenticula nicobarica, Denticulopsis hustedtii, Nitzschia miocenica, and Thalassiosira miocenica in the Miocene. This somewhat cosmopolitan assemblage gives way to a Pliocene and Holocene assemblage characterized by species such as Nitzschia kerguelensis, Thalassiosira inura, and Thalassiosira torokina, which are endemic to the Southern Ocean region. Samples examined from Prydz Bay are generally devoid of diatoms. The exception is Site 739, where diatoms occur sporadically in lower Oligocene and upper Miocene through Quaternary sediments. The Leg 119 diatom biostratigraphic results allow the development of a stratigraphic framework for the Indian sector of the Southern Ocean. This diatom zonation integrates diatom zonations developed previously for other sectors of the Southern Ocean. The zonation proposed here is based on biostratigraphic events of both geographically widespread and endemic species calibrated to the paleomagnetic stratigraphy. As such, this zonation has application throughout the Southern Ocean and allows correlation from the southern high latitudes to the low latitudes.